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10 Best Payment Processors for Shopify Stores in 2024

Kamso Oguejiofor Kamso OguejioforFinance Specialist April 03, 2024
April 03, 2024
Opening a Shopify store presents unique challenges, especially when it comes to choosing the right credit card processor. While Shopify does offer its own payment processing service, it’s not always the best solution. Many store owners have faced issues with Shopify Payments, like high monthly fees for advanced features, holds on funds or payouts, and a restrictive list of prohibited businesses and products.

Having said that, not all third-party payment processors will benefit your store. A poor integration with Shopify, high transaction fees, and a lack of support for fraudulent transactions will hinder your store’s operations. These issues, coupled with payment delays and limited payment options, can be a major roadblock for your store’s financial flow.

After thorough research, I found that Leaders Merchant Services (LMS) stands out as the best credit card processor for Shopify. LMS offers industry-low low fees, negotiable rates, and a dedicated chargeback assistance team. If these features sound appealing, you can contact LMS for a free quote. Or, if you’re curious about other options, keep reading to discover the other top credit card processors I’ve identified for Shopify.

Short on Time? These Are the Best Payment Processors for Shopify in 2024

  1. Leader Merchant Services1 – Negotiable rates with a meet-or-beat guarantee for Shopify store owners.
  2. Stax1 – Straightforward subscription-style model for busy Shopify stores.
  3. ProMerchant1 – Cost-saving plan for retail businesses and restaurants on Shopify.

See 7 More Great Options | Comparison Table

What We Look For in the Best Credit Card Processors for Shopify

In my search for the best credit card processors for Shopify store owners, I prioritized features and benefits that would offer the most value and efficiency for your online business.
  • Low transaction fees. Unlike Shopify Payments, most of the services I listed ensure you keep more of your earnings with low transaction and monthly fees. In addition to low fees, some of our card processors also offer free equipment when you open a merchant account, which can save you money if you also sell in person.
  • Fraud prevention and security. Every processor I chose provides effective security measures to protect you and your customers from fraud and data breaches. Also, some of the services I’ve listed have solid policies for reducing or preventing future chargebacks, which are common with Shopify stores.
  • Support for multiple payment methods. It’s essential to accommodate your customers’ payment preferences. Every service I’ve selected supports a variety of payment methods, including digital wallets and ACH.
  • Advanced e-commerce tools. Some of the processors on my list provide advanced marketing and accounting integrations to boost revenue and streamline your operations, as well as detailed transaction reports and analytics to help you make informed business decisions.
  • Reliable customer support. Unlike Shopify Payments, most of the processors on my list offer dependable customer support, ensuring that you have assistance whenever you need it.

Leaders Merchant Services (LMS) integrates with Authorize.net to provide a seamless connection with your Shopify store. I find Authorize.net provides a streamlined checkout experience by letting customers save their billing, payment, and shipping information for future use. In addition to its secure payment gateway, Authorize.net also provides a virtual terminal so you can accept payments over the phone, e-mail, or text.

As a Shopify store owner, you can benefit significantly from LMS’s negotiable rates. LMS has some of the lowest monthly and markup fees in the industry. Signing up for LMS requires a monthly fee of $9.00, which is very affordable for both low and medium-volume Shopify stores. Shopify Payments’ monthly fees, on the other hand, depend on your Shopify subscription plan, which typically starts from $32/month.

Security is another field LMS excels in. It’s PCI compliant and offers advanced fraud detection and prevention. This level of security is vital for your Shopify store, as it protects sensitive customer data and builds trust with your customers. What’s more, LMS has an entire department dedicated to helping you with chargeback issues.

Features and Benefits

  • POS equipment for your store. Unlike Shopify – which doesn’t offer any free equipment – LMS will give you free POS equipment when you sign up for a long-term contract. Also, as a certified Clover reseller, you can buy any of Clover’s advanced POS devices from LMS.
  • Meet-or-beat offer. If you’re currently processing payments elsewhere, LMS guarantees to meet or beat the pricing of your current credit card processor. You’ll have to give LMS a copy of your two most current processing statements, and if the company can’t beat or at least meet the price, it’ll give you a $200 gift card.
  • LMS funding. If you’re looking to grow your Shopify business or you’re just starting out, LMS offers cash advances. The best part is that you don’t have to put up any collateral because you can repay it through a small commission on future sales.
  • 98% approval rate. If you’ve struggled to find a payment processor due to low or no credit, give LMS a try. With one of the highest approval rates in the industry, there’s a good chance LMS will work with you.
Read our expert LMS review for more details.

Security features PCI compliant, advanced fraud detection and prevention, end-to-end encryption, tokenization
Payment methods accepted Credit and debit cards, digital wallets, ACH, bank transfers
24/7 support
Transaction fees on cheapest plan ~2.9% + 30¢
Monthly fee on cheapest plan $9.00

2. Stax: Straightforward Monthly Subscription Model1

Stax keeps it simple with a flat monthly subscription fee and zero markup on interchange fees for Shopify businesses. While the monthly subscriptions aren’t exactly cheap, if you run a high-volume store that sells many low-ticket items, you’ll only pay 0% + 10¢ (in-person) and 0% + 10¢ (online) per transaction.

Stax’s payment model is helpful if you want to know exactly how much you’ll pay each month, allowing for better budgeting and financial planning. Plus, many of Stax’s advanced processing solutions, including its proprietary payment gateway, is part of the monthly subscription. However, unlike CCP.com, to fully benefit from Stax and see savings of up to 40%, you’ll need to be processing at least $8,000 a month.

Stax enhances Shopify store management with robust analytics and inventory management features. The ability to access in-depth reporting is vital for any business looking to increase profits and maximize revenue. Stax’s unified dashboard allows you to compare product and service sales trends, giving you valuable insights to make data-driven decisions.

Features and Benefits

  • Free POS terminal of your choice. Depending on your business needs, you get a free Dejavoo, SwipeSimple, or PAX payment terminal.
  • Billing and invoicing. From your Stax dashboard, you’ll be able to schedule recurring billing and send your customers customized invoices and payment links by email or text.
  • QuickBooks integration. Unlike Shopify Payments, which doesn’t integrate directly with QuickBooks, Stax offers bi-directional syncing so your data will seamlessly transfer between Stax and QuickBooks, saving time on admin tasks and minimizing errors.
  • Zapier integration. Stax integrates seamlessly with Zapier which allows you to set up custom integrations. In addition to Shopify, you’ll also be able to connect to Slack, Mailchimp, HubSpot, Zoho Books, JotForm, and more.
For more details, check out our comprehensive Stax review.

Security features Level 1 PCI-compliant, multi-factor authentication, end-to-end encryption, tokenization, advanced fraud detection and prevention, payer verification
Payment methods accepted Credit and debit cards, selected digital wallets, ACH, bank transfers
24/7 support
Transaction fees on cheapest plan 0% + 10¢ (online)
Monthly fee on cheapest plan $99.00
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3. ProMerchant: Best for Retail and Restaurants on Shopify

ProMerchant is a great choice for retail businesses and restaurants on Shopify. Its custom Zero Cost Processing Plan for these industries allows you to pass credit card processing fees to your customers through a surcharge. While this allows you to protect most of your profit margins, you do need to be transparent with your card-paying customers so that they’re aware of the additional fees.

If you’re a restaurant or retail store with a Shopify website, you can take advantage of ProMerchant’s generous free POS options, which include a free Verifone, Payanywhere, PAX, or Ingenico terminal. The PAX A920, in particular, is well-suited for a busy retail or restaurant operation. It allows you to print out receipts, capture signatures on the touchscreen, add tips, and view transaction history and inventory management.

ProMerchant lets you email invoices to your customers, complete with a “click to pay” link. This feature provides your customers with convenience as it helps streamline the payment process by letting your customers securely pay via browser or mobile. What’s more, ProMerchant can help you send out friendly reminders to customers that are yet to fulfill their invoices.

Features and Benefits

  • AI-powered product recommendations. ProMerchant uses AI to analyze browsing patterns, user behavior, and purchase history of each person that visits your Shopify store. It then uses this analysis to recommend personalized products to each visitor.
  • One-page checkout. You can streamline your customers’ checkout process with ProMerchant’s one-page checkout. Your customer only needs to enter their billing, shipping, and payment information on one page.
  • Automatic billing. Through ProMerchant’s integration with Authorize.net, you’ll be able to access advanced recurring and subscription billing. This allows you to bill customers on their preferred schedule (monthly, weekly, or custom) while ensuring you’ll never miss a payment.
  • High-risk merchant accounts. Your Shopify store might be high-risk if, for instance, you sell certain types of products or process high-risk transactions. Fortunately, ProMerchant’s high risk accounts come with all the same features and services as low-risk accounts, including fraud protection, integration with Authorize.net, and more.
Learn more about ProMerchant in our full review.

Security features PCI compliant, end-to-end encryption, advanced fraud detection and prevention, tokenization, payer verification
Payment methods accepted Credit and debit cards, ACH, digital wallets, bank transfers
24/7 support
Transaction fees on cheapest plan 3% + 10¢ (credit)
Monthly fee on cheapest plan $7.95

4. Flagship Merchant Services: Fastest Payouts to Shopify Merchants

Flagship Merchant Services is your best solution for same-day payouts for your Shopify store. It might cost extra, but I’d say the means to get your funds right away is well worth the investment – especially when compared to Shopify Payments’ fastest payout period of 1 business day, with most payout periods typically 2-3 days.

Another great thing about Flagship is that you can get your account approved in a couple of hours and start receiving payments on your Shopify store. The onboarding is pretty straightforward. You don’t need to provide several documents nor do you get asked many questions — you just fill out some basic information, and you’re good to go.

MobilePay by PaySafe, Flagship’s free mobile app, lets you accept keyed-in payments through your phone. Whether you’re at a trade show, pop-up shop, or simply away from your computer, you can still process payments for your Shopify store with ease. That said, Flagship’s interchange-plus fees (3.98% + 0.21¢ (online)) are on the pricier side – Leaders Merchant Services is more affordable.

Features and Benefits

  • iAccess business management portal. This free software provides essential analytics for your Shopify store, helping you track sales volume, chargebacks, and analyze competitors. Understanding these metrics is important for making informed business decisions.
  • Digital loyalty program. With Flagship, you can reward loyal customers, which is a good way to stand out in a competitive market. It also encourages repeat purchases and helps you build a dedicated customer base for your Shopify store.
  • Secure e-commerce transactions. Flagship’s payment gateway, Authorize.net, ensures safe and convenient online transactions with features like AVS and CVV2. Also, as a Flagship merchant, you’ll get access to Authorize.net at a discount price of $7.95.
  • Free credit card terminal. You get a free credit card terminal when you sign a long-term contract with Flagship. While it’s technically not “free” (you’ll have to return it when your contract ends), it does provide a cost-effective solution for in-person Shopify retailers.
Our comprehensive Flagship review has more info on rates.

Security features PCI compliant, tokenization, end-to-end encryption, advanced fraud detection and prevention, payer verification
Payment methods accepted Credit and debit cards, ACH, bank transfers, digital wallets
24/7 support
Transaction fees on cheapest plan 1.98% + 0.21¢ (online)
Monthly fee on cheapest plan $7.95

5. CreditCardProcessing.com: Best for High-Volume Shopify Stores

CreditCardProcessing.com (CCP.com) offers a simple monthly subscription plan with no percentage-based markup starting from 0% + 30¢ (Starter) for $15.00/month. Like most subscription plans, you’ll pay more per month in exchange for lower interchange-plus transaction rates. This pricing model makes the most sense for Shopify businesses that sell high ticket items at high sales volumes. Low- to mid-volume stores are better off with Leaders Merchant Services or PAYARC.

One of CCP.com’s standout features is its free access to the premium Vindicia subscription management platform. It’s a great tool for handling any recurring payment plans your Shopify store offers and you’ll receive essential analytics to optimize your subscription plans. You also get Vindicia Retain, a service that can recover up to 30% of failed credit card transactions.

Another unique feature of CCP.com is its account updater functionality. By keeping card data up to date in your Customer Information Manager (CIM) profiles and Automated Recurring Billing (ARB) subscriptions, CCP.com ensures smooth transactions, reduces payment failures, and improves the overall customer experience.

Features and Benefits

  • Free POS terminals. You’ll get a free portable Pax A920 POS terminal when you commit to a yearly contract. CCP.com also offers a free Clover terminal on its Premier plan and above.
  • Advanced security features. CCP.com provides the ability to enforce IP bans for specific countries and set daily and hourly transaction limits. It automatically verifies customer data and checks for any discrepancies before processing a purchase.
  • Data breach protection. Every CCP.com plan includes up to $100,000 in insurance for financial losses resulting from a data breach.
  • High approval rates. CCP.com offers one of the highest approval rates in the US. Unlike most credit card processors that charge you extra fees if you have a low credit score, CCP.com gives you access to the same features as other merchants for the same price.
Read our full CreditCardProcessing.com review for more details.

Security features Level 1 PCI compliant, end-to-end-encryption, data breach insurance, tokenization, advanced fraud detection and prevention, payer verification
Payment methods accepted Credit and debit cards, digital wallets, ACH, bank transfers
24/7 support
Transaction fees on cheapest plan 0% + 0.05¢ (High volume)
Monthly fee on cheapest plan $15.00

6. PAYARC: Flexible Plans for Small and Large Shopify Stores

PAYARC offers an efficient membership plan for Shopify stores with high sales volumes. Shopify businesses generating $25,000 or less will pay a flat interchange-plus fee of 0% + 15¢ (in-person & online) – and the more you sell, the lower the rate. PAYARC also offers a competitive flat rate plan for lower-volume or new business with no monthly fees and 2.9% + 30¢ (online) per transaction.

PAYARC smoothly integrates with major payment gateways like Authorize.net and NMI, both of which allow you to accept payments on your Shopify store. Impressively, PAYARC accepts payments in 150 currencies across 47 countries through Planet Payment, whereas Shopify Payments only supports 23 countries.

PAYARC allows you to integrate and streamline your online payment systems with its free API and software development kit. Once you get your API token from your dashboard, you can incorporate advanced functionalities like tiered pricing, custom invoices, and recurring or usage-based billing into your Shopify store.

Features and Benefits

  • Smart POS terminals and systems. PAYARC uses PAX POS terminals that run on Android technology and come with features like a magstripe reader, Wi-Fi and Bluetooth connections, a camera, built-in GPS, and more.
  • Quick access to funds. PAYARC offers a standard payout time of 24-48 hours but also provides a same-day payout option for an additional fee. Quick payout times are vital for maintaining cash flow and PAYARC ensures your business has enough money to run smoothly and meet customer demands quickly.
  • Low-cost processing for nonprofits. PAYARC offers special reduced processing rates for nonprofits. Coupled with Shopify’s NPO plans, this could mean significant savings for your cause.
  • POS equipment integration. If you prefer not to use its hardware, PAYARC can try to integrate your existing POS equipment with its platform, which can help you save costs. However, this doesn’t work for all POS brands.
For more information, read our expert PAYARC review.

Security features PCI compliant, end-to-end encryption, tokenization, fraud monitoring and prevention
Payment methods accepted Credit cards, debit cards, ACH, digital wallets (Apple Pay and Google Pay only)
24/7 support
Transaction fees on the cheapest plan 0% + 15¢ (in-person & online)
Monthly fee on cheapest plan $69.00

Other Notable Credit Card Processors for Shopify

7. Pay.com

Unlike other payment processors that require third-party integrations, Pay.com directly syncs with Shopify, streamlining the setup process for your store. You’ll be able to curate a list of preferred payment methods for your store, with options ranging from credit and debit cards to digital wallets like Google Pay and Apple Pay. Plus, you can easily customize the checkout page for your Shopify store to present a consistent and professional online presence.

Pay.com’s pricing is straightforward but not necessarily cost-effective for all Shopify stores. It offers a simple flat pricing model with no monthly fees, which appeals to new or small businesses. However, the per-transaction fees (2.9% + 29¢) are higher compared to some competitors, making it less suitable for high-volume businesses. Also, Pay.com’s payout time varies and can take up to 7 business days, depending on your store’s revenue and estimated risk level.

8. Square1

Once you’ve created your Square account, you can easily integrate it with your Shopify store using Zapier. You should, however, take note of complaints from Square merchants about frozen accounts and unexpected account terminations — it’s important to complete your profile thoroughly to avoid any issues with payment processing. Also, while Square’s flat rate pricing is very transparent, it’s definitely a bit costly, with online payments starting from 2.6% + 10¢.

Square offers an FDIC-insured business checking account that’s easy to set up, with no credit checks or cumbersome paperwork. This account is free from common banking fees like monthly or overdraft charges, and it integrates seamlessly with your Square account. You can sign up for a free Square account and start accepting payments on the same day, eliminating the usual delays in getting a business off the ground.

9. Chase Payment Solutions1

In addition to offering a payment gateway through Authorize.net, Chase Payment Solutions also has an Orbital Virtual Terminal for keyed-in transactions. Through this software, you’ll be able to process sales, refunds, and voids. What’s more, you can use the virtual terminal to manually manage payment functions like splitting of shipments and settlement of marked transactions and batches.

Same-day funding with Chase is only available if you have a Chase Business Banking account, which costs $15/month. However, if you maintain a minimum daily balance of $2,000 in your account, Chase may waive these extra costs – so you could potentially get same-day funding for free. That said, Chase does have mixed customer reviews about unexpected account closures, so I’d recommend reading the fine print before signing up.

10. POS Pros1

POS Pros offers solutions ideal for hybrid Shopify businesses with brick-and-mortar stores. After an initial consultation with a POS Pros Specialist, you’re invited to try different POS solutions that fit your specific business model. This personalized approach ensures you get the right equipment for managing your in-store operations.

Like most card processors on my list, POS Pros uses the reliable Authorize.net as its virtual terminal and payment gateway. You’ll receive access to various features, including fraud detection and the ability to create and send digital invoices to your customers. However, it’s important to note that POS Pros’ pricing lacks transparency and you’ll have to pay for extras like a non-PCI compliance fee and software fees to use Authorize.net.

The Best Payment Processors for Shopify Will Save You Money

Selecting the right credit card processor for your Shopify store can be overwhelming, with so many options offering similar features. It’s crucial to find one that aligns with your specific business needs.

If you’re looking for a credit card processor that simplifies payments for returning customers, enhances your checkout process, and offers negotiable rates, I recommend Leaders Merchant Services (LMS)1. It integrates with Authorize.net for easy repeat payments and encourages you to negotiate your rates.

Meanwhile, if you run a retail business or restaurant on Shopify, you should consider ProMerchant. It offers a unique Zero Cost Processing plan for restaurants and retail businesses that allows you to pass processing fees to your card-paying customers. It also offers fraud mitigation plans for high-risk merchants.

For established and new Shopify stores alike, PAYARC is a great option. Its membership plans offer low transaction fees that are suitable for high-volume Shopify businesses, while its flat rate plan is ideal if you process less than $7,000/month. PAYARC also accepts 150 currencies and offers quick payout times, which are essential for maintaining cash flow.

Here’s a quick breakdown of the best credit card processors for Shopify.
Best Feature Best For Monthly fee on cheapest plan Transaction fees on cheapest plan
Leaders Merchant Services Industry-low fees and negotiable rates for new and established businesses Shopify store owners who want to negotiate rates to best suit their budget $9.00 ~2.9% + 30¢
ProMerchant Savings for retail and restaurants with custom zero-cost processing program Retail businesses and restaurants on Shopify $7.95 3% + 10¢ (credit)
Stax Advanced e-commerce and business tools included in monthly subscription High volume Shopify stores generating over $8,000 a month $99.00 0% + 10¢ (online)
Flagship Merchant Services Fast onboarding with option for same-day funding New Shopify businesses that want to start receiving payments as soon as possible and need a steady cash flow $7.95 1.98% + 0.21¢ (online)
CreditCardProcessing.com Access to premium Vindicia subscription management service Shopify stores looking for robust subscription solutions $15.00 0% + 0.05¢ (High volume)
PAYARC Third-party payment gateway that supports processing in 150 currencies Shopify stores looking to sell internationally $69.00 0% + 15¢ (in-person & online)


What payment processor should I use for Shopify?

I recommend Leaders Merchant Services (LMS) — it’s the best overall credit card processor for Shopify. LMS integrates with Authorize.net, allowing you to easily connect your Shopify store. It also offers cheap monthly fees and encourages merchants to negotiate the best rates for their business. To keep your Shopify store safe, LMS is PCI compliant, it provides advanced fraud detection, and has dedicated support for chargeback issues.

Does Shopify have a credit card processor?

Yes, Shopify offers its own processing solution in the form of Shopify Payments. However, many store owners have complained about issues like holds on funds or delayed payouts, with typical payout times somewhere between 2-3 days. On the other hand, Flagship Merchant Services is a good option for quick funding with optional same-day payouts for an additional fee.

Can I use my own payment processor with Shopify?

Yes, you can use your own payment processor with Shopify, although you’ll have to pay an extra fee to use a third-party solution. I recommend Leaders Merchant Services (LMS) as the best option for your store. LMS features low industry rates and negotiable plans, making Shopify’s extra fee worth it in return for substantial savings on your processing fees.

How much does Shopify charge per sale?

Shopify charges a per transaction fee ranging from 2.4% to 2.9% + $0.30, depending on your plan. I recommend CreditCardProcessing.com as a cost-effective alternative for high-volume Shopify stores. It offers membership pricing with online transaction fees starting at 0% + 30¢ (Starter) and a small monthly fee of $15.00, making it a more budget-friendly option for your Shopify business.

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